Emergence Of New Diseases Research Articles

The Story behind COVID-19: Animal Diseases at the Crossroads of Wildlife, Livestock and Human Health

A number of virological, epidemiological and ethnographic arguments suggest that COVID-19 has a zoonotic origin. The pangolin, a species threatened with extinction due to poaching for both culinary purposes and traditional Chinese pharmacopoeia, is now suspected of being the “missing link” in the transmission to humans of a virus that probably originated in a species of bat. Our predation of wild fauna and the reduction in their habitats have thus ended up creating new interfaces that favour the transmission of pathogens (mainly viruses) to humans. Domesticated animals and wild fauna thus constitute a reservoir for almost 80% of emerging human diseases (SARS-CoV, MERS-CoV, Ebola). These diseases are all zoonotic in origin. As if out of a Chinese fairy tale, the bat and the pangolin have taught us a lesson: within an increasingly interdependent world, environmental crises will become ever more intertwined with health crises. Questions relating to public health will no longer be confined to the secrecy of the physician’s consulting room or the sanitised environment of the hospital. They are now being played out in the arena of international trade, ports and airports and distribution networks. Simply put, all human activity creates new interfaces that facilitate the transmission of pathogens from an animal reservoir to humans. This pluri-disciplinary article highlights that environmental changes, such as the reduction in habitats for wild fauna and the intemperate trade in fauna, are the biggest causes of the emergence of new diseases. Against this background, it reviews the different measures taken to control, eradicate and prevent the emergence of animal diseases in a globalised world.

Coronavirus (SARS-CoV-2): Preventions, keys to diagnosis and treatment of SARS-CoV-2

World Health Organization (WHO) is gathering the latest scientific findings and knowledge on coronavirus disease (SARS-CoV-2) and compiling it in a database. WHO update the database daily from searches of bibliographic databases, hand searches of the table of contents of relevant journals, and the addition of other relevant scientific articles that come to our attention. The entries in the database may not be exhaustive and new research will be added regularly. Nobel coronavirus investigators, the recognition of a nobel coronavirus as the cause of severe acute respiratory syndrome (SARS) was certainly remarkable, yet perhaps not surprising. Advances in the biology of coronaviruses have resulted in greater understanding of their capacity for adaptation to new environments, transspecies infection, and emergence of new diseases. New tools of cell and molecular biology have led to increased understanding of intracellular replication and viral cell biology, and the advent in the past five years of reverse genetic approaches to study coronaviruses has made it possible to begin to define the determinants of viral replication, transpecies adaptation, and human disease. This summary will discuss the basic life cycle and replication of the well-studied coronavirus, mouse hepatitis virus (MHV), identifying the unique characteristics of coronavirus biology and highlighting critical points where research has made significant advances, and which might represent targets for antivirals or vaccines. Areas where rapid progress has been made in SCoV research will be described. Finally, areas of need for research in coronavirus replication, genetics, and pathogenesis will be summarized.

Are substrate-mediated microbial community shifts the future of soilborne disease management?

The loss of methyl bromide as a soil fumigant, the limited efficacy of alternative fumigants, and the emergence of new diseases has necessitated fumigant-based crop production systems to radically restructure for continued productivity. In the coastal valleys of central California, the principal objective of soil fumigation has been to confine Verticillium dahliae population densities to levels below the threshold at which yield losses occur. The wide-spread adoption of alternative fumigants has coincided with the emergence of soilborne diseases caused by Fusarium oxysporum f. sp. fragariae and Macrophomina phaseolina. The ability to harness native soil microbiomes to manage plant pathogens remains a promising but relatively unexplored area. Our studies have focused on substrate-mediated changes in soil prokaryote communities with the goal to convert Verticillium wilt-conducive soils to Verticillium wilt-suppressive soils. The effect of broccoli residue and crustacean meal on soil microbiomes and suppression of Verticillium wilt were studied in soils with distinct land-use histories: intense agriculture, transition from pasture to agriculture, and native, undisturbed soil. Regardless of the soil type, the organic inputs significantly reduced V. dahliae microsclerotia and wilt incidence and severity on eggplants in the greenhouse, and these reductions were correlated with an increase in the proportion of known fungal antagonists. Prokaryote communities identified were distinct in the wilt-suppressive soils as compared to the wilt-conducive soils. Three cycles of inputs nearly eliminated the pathogen in all three soil types. This approach was validated in a 12.2 ha commercial lettuce field in Salinas Valley with a known history of severe Verticillium wilt. After an 18-month broccoli-Romaine lettuce-broccoli rotation including amending soil with crustacean meal before each crop, significant reductions in V. dahliae microsclerotia density were achieved. These studies demonstrated the potential for harnessing native soil microbiomes to manage plant pathogens using specific carbon sources that favor fungal antagonists. This approach worked in soils with various land use and disease incidence histories and was validated in a commercial lettuce field in Salinas Valley, California.

Molecular detection of Rickettsia spp., Borrelia spp., Bartonella spp. and Yersinia pestis in ectoparasites of endemic and domestic animals in southwest Madagascar

Little is known about the presence of vector-borne bacteria in southwest Madagascar. Anthropogenic alteration of natural habitats represents an important driver for the emergence of new diseases. Especially the involvement of livestock and the involuntary maintaining of invasive synanthropic animals (particularly rats) facilitate disease transmission from wildlife to humans and associated animals and vice versa. The dissemination or acquisition of ectoparasites is most likely in regions where human/wildlife contact is increasing. Little is known about the presence of vector-borne bacteria in southwest Madagascar. In 2016 and 2017, ectoparasites were collected from various introduced (cattle and goats, cats, dogs and chicken, rats and mice) and native animal species (mouse lemurs [Microcebus griseorufus], Grandidier's mongooses [Galidictis grandidieri], bastard big-footed mice [Macrotarsomys bastardi], greater hedgehog tenrecs [Setifer setosus] and lesser hedgehog tenrecs [Echinops telfairi]) in the northern portion of Tsimanampetsotsa National Park and the adjacent littoral region. Thirteen species of blood-feeding ectoparasites (235 individuals of ticks [5 species], 414 lice [4 spp.] and 389 fleas [4 spp.]) were investigated for the presence and identity of rickettsiae, borreliae, bartonellae and Yersinia pestis using PCR techniques. Rickettsia spp. were detected in every single ectoparasite species (Amblyomma variegatum, A. chabaudi, Rhipicephalus microplus, Haemaphysalis simplex, Argas echinops, Ctenocephalides felis, Echidnophaga gallinacea, Pulex irritans, Xenopsylla cheopis, Haematopinus quadripertusus, Linognathus africanus, L. vituli, Lemurpediculus verruculosus). Lice and ticks were found harboring rickettsiae identified as Rickettsia africae, while Rickettsia felis-like bacteria were associated with fleas. Borrelia spp. were detected in 5% of H. simplex and 1% of R. microplus ticks. Bartonella spp. were detected in 40% of H. quadripertusus pools and in 5% of L. verruculosus pools. Y. pestis was detected in X. cheopis and E. gallinacea fleas collected from a rat. This study presents the detection of a broad spectrum of vector-borne bacteria including potential pathogens, and an unexpected finding of Y. pestis far off the known plague foci in Madagascar.

Lichens − masters of extraordinary symbiosis with potent pharmaceuticals

Lichens are an excellent example of a symbiotic relationship between members belonging to two unrelated separate kingdoms (fungi and algae), which results in the collection of secondary metabolites. These metabolites can be fungal originated, algal originated, or unique compounds not produced by either fungi or algae individually. Although involved since centuries in traditional folk medicine, lichens have attracted extra attention of scientists owing to the emergence of new diseases, which has required screening for novel compounds capable of curing or supporting currently used compounds. This review highlights the nature, importance, nutritional and pharmaceutical uses, and applications of these enigmatic dual organisms.

PREVENTION OF ARTHROPOD-VECTOR OF INFECTIOUS DISEASES BY INSECT REPELLENTS AND OTHER MEASURES

The bloodsucking arthropod bite is the cofactor in the transmission of infectious diseases to man and animals. They release with saliva powerful anti-homeostatic and immuno-modulators that favor the replication and the establishment of the infective pathogen. The transmission depend on the close contact of the child with a seropositive mother (or relatives) whose infective saliva is used to relieve itching and scratching at the arthropod bite's sites. Vector-borne diseasesare caused by parasites, bacteria or viruses transmitted by the hematophagous arthropods bite (mainly ticks and mosquitoes). The past decades there were emergence of new diseases or re-emergence of existing diseases, due to changes in their epidemiology (i.e. geographical distribution, prevalence, pathogenicity and vector-capacity). Besides, human factors, such as travel with pets, changes in human habitats, social and leisure activities have their input, but climate changes also have a direct impact on arthropod vectors. Vaccinations are up to date for diseases prevalent in the area, but what about diseases beyond vaccination? Wear light-colored, long-sleeved shirts and long trousers, tucked into socks or boots, and the use of insect repellent on exposed skin and clothing to protect from being bitten by mosquitoes, sandflies and/or ticks. This review discussed the vectors, diseases and feasible insecticidal control.

Recent advances in microfluidics for drug screening.

With ever increasing drug resistance and emergence of new diseases, demand for new drug development is at an unprecedented urgency. This fact has led to extensive recent efforts to develop new drugs and novel techniques for efficient drug screening. However, new drug development is commonly hindered by cost and time span. Thus, developing more accessible, cost-effective methods for drug screening is necessary. Compared with conventional drug screening methods, a microfluidic-based system has superior advantages in sample consumption, reaction time, and cost of the operation. In this paper, the advantages of microfluidic technology in drug screening as well as the critical factors for device design are described. The strategies and applications of microfluidics for drug screening are reviewed. Moreover, current limitations and future prospects for a drug screening microdevice are also discussed.

Two Is Better Than One: Studying Ustilago bromivora-Brachypodium Compatibility by Using a Hybrid Pathogen.

Pathogenic fungi can have devastating effects on agriculture and health. One potential challenge in dealing with pathogens is the possibility of a host jump (i.e., when a pathogen infects a new host species). This can lead to the emergence of new diseases or complicate the management of existing threats. We studied host specificity by using a hybrid fungus formed by mating two closely related fungi: Ustilago bromivora, which normally infects Brachypodium spp., and U. hordei, which normally infects barley. Although U. hordei was unable to infect Brachypodium spp., the hybrid could. These hybrids also displayed the same mating-type bias that had been observed in U. bromivora and provide evidence of a dominant spore-killer-like system on the sex chromosome of U. bromivora. By analyzing the genomic composition of 109 hybrid strains, backcrossed with U. hordei over four generations, we identified three regions associated with infection on Brachypodium spp. and 75 potential virulence candidates. The most strongly associated region was located on chromosome 8, where seven genes encoding predicted secreted proteins were identified. The fact that we identified several regions relevant for pathogenicity on Brachypodium spp. but that none were essential suggests that host specificity, in the case of U. bromivora, is a multifactorial trait which can be achieved through different subsets of virulence factors.

Porcine Anti-viral Immunity: How Important Is It?

Pork has become the number one meat consumed worldwide. Meeting the demand for pork has forced the revolution of swine production from traditional husbandry practices that involved a few pigs or small herds to intensive concentration of swine raised in multisite production systems. This dramatic change has made the production of pork very efficient, but it has also changed the ecology of many swine diseases, may encourage the emergence of new diseases, and amplifies the economic impact of swine diseases. Sustained treatment of diseases in livestock production is not feasible making prevention of disease a priority. Prevention of livestock diseases involves eliminating exposure to pathogens and anti-viral strategies to prevent or reduce clinical disease. For some swine diseases, efficacious vaccines can be made, however, for other diseases the host/pathogen relationship is more complex and efficacious vaccines are not available. Given the increasing demand for pork, the development of new approaches to improve swine anti-viral immunity is critical. Rate-limiting steps to improving vaccines are understanding how the pathogen interacts with the host's immune system, any immunopathology resulting from such interactions and how the host's immune system resolves the infection. Solving this puzzle will require sustained research and may require new technologies to battle contemporary diseases now wreaking havoc in swine production systems around the world. This Special Issue will focus on current swine viral diseases that are the most challenging to the global production of pork with contributions focusing on anti-viral immunity.

Trichoderma and Its Prospects in Agriculture of Nepal: An Overview

In the world, the traditional agricultural practices are getting affected by various problems such as disease, pest, drought, decreased soil fertility due to use of hazardous chemical pesticides, pollution and global warming. As a result, there is a need for some eco-friendly bio-control agents that help in resolving the previous mentioned problems. The various types of biological control agents such as bacteria and fungi are involved in bio-control activity. Among them, fungal genus Trichoderma plays a major role in controlling the plant diseases. Species of Trichoderma are diverse fungal microbial community known and explored worldwide for their versatilities as biocontrol and growth promoting agents. These fungi reproduce asexually by production of conidia and chlamydospores and in wild habitats by ascospores. Trichoderma species are efficient mycoparasites and prolific producers of secondary metabolites, some of which have clinical importance. However, the ecological or biological significance of this metabolite diversity is sorely lagging behind the chemical significance. Several Trichoderma spp. positively affect plants by stimulating plant growth, and protecting plants from fungal and bacterial pathogens. They are used in biological plant protection as bio-fungicides as well as in bioremediation. A large number of research groups are working on various aspects of Trichoderma viz., diversity, ecology and their applications. The capacity of Trichoderma fungi to produce lytic enzymes is used in animal feed, and wine making and brewery industries. Trichoderma spp. are the most successful bio-control agents as more than 60% of the registered bio-fungicides used in today’s agriculture belongs to Trichoderma -based formulation. The increase in incidence and severity of diseases and emergence of new diseases causes the significant yield losses of different crops in Nepal. But the research and studies on plant diseases are limited.
 Int. J. Appl. Sci. Biotechnol. Vol 7(3): 309-316

Bactericidal Efficacy of Selected Medicinal Plant Crude Extracts and their Fractions against Common Fish Pathogens

The emergence of new diseases and the increased use of antibiotics have led to the development of resistant bacterial strains. Thus, there is greater attention to seek new antibacterial agents from the natural sources for combating fish diseases in the aquaculture industry. The present study evaluated the bactericidal efficacy of crude methanolic and aqueous extracts from Polygonum chinense, Syzygium polyanthum, Premna foetida, Pimenta dioica, Brucea javanica, Vitex negundo, Alpinia conchigera and Clinacanthus nutans against Vibrio harveyi, Vibrio alginolyticus, Vibrio parahaemolyticus and Aeromonas hydrophila using disc diffusion method. The results showed that methanolic extracts of P. dioica, P. foetida and P. chinense, and aqueous extracts of P. dioica and S. polyanthum showed moderate to strong activity (10.8 to 17.2 mm) against all the tested bacteria. These five potential crude extracts were fractionated using liquid-liquid extraction method to obtain the methanol, dichloromethane and ethyl acetate fractions. Among the fractions, ethyl acetate fraction showed the highest activity against all tested bacteria, with minimum inhibition concentration (MIC) values between 0.625 and 10.000 mg/mL. In addition, the five potential crude extracts had low to moderate toxicity with LC50 >100 μg/mL using brine shrimp cytotoxicity assays. The results of this study indicated that methanolic extracts of P. chinense and P. foetida that showed high bactericidal activity and low toxicity could be good potentials for use in fish culture.

OSCAR, a national observatory to support the durable deployment of disease-resistant grapevine cultivars

The cultivation of disease-resistant grapevine cultivars makes it possible to reduce considerably the number of pesticide treatments applied in viticulture. The recent, but increasingly widespread deployment of these cultivars raises several important issues. The first concerns the qualitative potential of the cultivars and their marketing. The second issue is more generally important and concerns the management of durability of resistance. Several cases of erosion or breakdown of resistance have already been reported in Europe. The evolution of pathogen populations targeted by varietal resistance should therefore be closely monitored, to ensure that grapevine resistance remains effective in the long term. Another key issue is the design of the cropping system, which should be adapted to resistant cultivars so as to maintain production objectives, promote the durability of resistance and minimize the use of pesticides. INRA has set up the National Observatory for the Deployment of Resistant Cultivars (OSCAR; http://observatoire-cepages-resistants.fr) to meet these challenges. OSCAR is a participative network based on plots in production situations planted by growers. The participative dimension of the network promotes the sharing of experiences relating to agronomic behavior, the potential for mechanization, ease of cultivation and wine quality. This observatory also monitors the emergence of new diseases or of virulent strains. Powdery and downy mildew (diseases targeted by varietal resistance) isolates are collected and tested under laboratory conditions, to monitor changes in population aggressiveness. We present here the first results obtained for the 34 plots of OSCAR monitored in 2017. This observatory is currently being extended to a larger number of plots in France and other European countries. The data obtained will be fed into mathematical models to determine the effects of deployment strategies and landscape features on the epidemiological dynamics of resistance erosion.

Emerging respiratory infections: The infectious disease pathology of SARS, MERS, pandemic influenza, and Legionella.

Lower respiratory infections remain one of the top global causes of death and the emergence of new diseases continues to be a concern. In the first two decades of the 21st century, we have born witness to the emergence of newly recognized coronaviruses that have rapidly spread around the globe, including severe acute respiratory syndrome virus (SARS) and Middle Eastern respiratory syndrome virus (MERS). We have also experienced the emergence of a novel H1N1 pandemic influenza strain in 2009 that caused substantial morbidity and mortality around the world and has transitioned into a seasonal strain. Although we perhaps most frequently think of viruses when discussing emerging respiratory infections, bacteria have not been left out of the mix, as we have witnessed an increase in the number of infections from Legionella spp. since the organisms’ initial discovery in 1976. Here, we explore the basic epidemiology, clinical presentation, histopathology, and clinical laboratory diagnosis of these four pathogens and emphasize themes in humans’ evolving relationship with our natural environment that have contributed to the infectious burden. Histology alone is rarely diagnostic for these infections, but has been crucial to bettering our understanding of these diseases. Together, we rely on the diagnostic acumen of pathologists to identify the clinicopathologic features that raise the suspicion of these diseases and lead to the early control of the spread in our populations.

Two conifer species native to Patagonia threatened by Phytophthora austrocedri

AbstractPhytophthora austrocedri is a pathogen of Austrocedrus chilensis causing “Mal del Ciprés” (cypress sickness) in Patagonia and killing Juniperus communis in Britain, along with other species in the Cupressaceae. The evident association of the pathogen with members of the Cupressaceae makes it necessary to study the susceptibility of other species related to A. chilensis to prevent the emergence of new diseases. The present study tested the pathogenicity of P. austrocedri to three native and endemic conifers in South America: Fitzroya cupressoides, Pilgerodendron uviferum and Araucaria araucana. The results showed that F. cupressoides and P. uviferum were highly susceptible to P. austrocedri. Since these are endangered tree species, the outcome of this study is crucial for governmental agencies, policymakers and stakeholders.

Intellectual Property Rights (IPR) issues related to access and use of genetic resources

Genetic Resources (GR) refer to genetic material of actual or potential value. Use of GR refers to the process of researching their beneficial properties and using them to increase scientific knowledge and understanding, or to develop commercial products. There is continuous search for newer resources to meet the future demands that arise with the emergence of new diseases, abiotic stresses, climate change, and enhanced demand for food and nutritional security. GR are exchanged and searched continuously for specific traits to improve yields and nutritional value in crops and animal genetic resources. Every nation is concerned with acquisition of diverse and superior germplasm for conservation and utilization. The rapid advancements in the fields of molecular biology, biotechnology and bioinformatics, led to the emergence of new legal, political and technological regimes regulating access to GR. Three international negotiations impacted the access to GR, these are the Convention on Biological Diversity (CBD), the Agreement on Trade-Related Aspects of Intellectual Property Rights (TRIPS) as part of the Agreement establishing the World Trade Organization (WTO) and the International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA). The regulation regarding access to GR, increasing application of IPRs and the vast potential of biological wealth yet to be tapped through bio-prospecting and genetic engineering, has placed greater demands on nations to adjust to the changing scenario of GR management. Currently access to GR is under the provisions of CBD and access to GR is based on mutually agreed terms (MAT), subject to prior informed consent (PIC). In response to CBD, India enacted the Biological Diversity Act (BDA), 2002 and established the National Biodiversity Authority (NBA) in 2003. Access to PGR from India is therefore regulated by BDA, 2002. The Nagoya Protocol which entered into force from October 2014 defines the international regime within the framework of CBD to promote and safeguard the fair and equitable sharing of benefits arising from the utilization of genetic resources. The paper discusses these agreements in detail with reference to access and use of GR.

Comorbidities in inflammatory joint and spine diseases in XXI century.

The evaluation the occurrence of comorbidities in patients with inflammatory diseases of the spine and joints and the assessment of the general changes in comorbidities at the beginning of the XXI century compared to previous period. Comorbidity was analyzed in 245 patients with spondyloarthritis who participated in the scientific program PROGRESS. Validated comorbidity assessment indices were used in the study. The analysis of 96 sources of literary bases RISC and PubMed were used in literature analysis. The results of their own observation and literary search were compared. According to the patients' cards, an analysis of the structure of comorbidities was conducted in 221 patients: 207 (93.66%) patients with spondyloarthritis had two or more comorbidities. The most common diseases were diseases of gastrointestinal tract (60.6%) and cardiovascular pathology (58.3%), secondary osteoarthritis (60.2%). According to literature sources, most of the comorbidities and spondyloarthritis are interrelated pathogenetically and undergo a change in the profile of rheumatic and/or related diseases undergo simultaneous changes. The emergence of new diseases in the structure of comorbidity and new drugs requires the development of recommendations that take into account the presence of comorbidity in patients with a rheumatic diseases. Most patients with spondyloarthritis has comorbidity. The change in rheumatic and non-rheumatic diseases that occurs in the 21st century has a mutual influence, changing the profile of patients and determining the change in the tactics of their management.

What is epidemiology? Changing definitions of epidemiology 1978-2017.

ContextEpidemiology is a discipline which has evolved with the changes taking place in society and the emergence of new diseases and new discipline related to epidemiology. With these evolutions, it is important to understand epidemiology and to analyse the evolution of content of definitions of epidemiology.ObjectivesThe main objective of this paper was to identify new definitions of epidemiology available since 1978. Secondary objectives were to analyse the content of these definitions, to compare them with those used by Lilienfeld and to determine whether changes have taken place over the last forty years.MethodsA review of grey literature and published literature was conducted to find the definitions of epidemiology written between 1978 and 2017.Results102 definitions of epidemiology were retained. They helped to highlight 20 terms and concepts related to epidemiology. Most of them were already used in the definitions used by Lilienfeld. Five terms were present in more than 50% of definitions from the period 1978 to 2017: “population”, “study”, “disease”, “health” and “distribution”. Several developments have occurred: strengthening of the terms “control” and “health” already used, the concept of “disease” was less frequently encountered whereas the concepts “infectious diseases”, “mass phenomenon” are no longer used in definitions from 1978 to 2017.ConclusionThis evolution of content of definition of epidemiology is absent from books on epidemiology. A thematic analysis of definitions of epidemiology could be conducted in order to improve our understanding of changes observed.

A Bibliometric Analysis of Clinical and Translational Research in Pediatric Gastroenterology From 1970 to 2017.

Pediatric gastroenterology is a clinical and research discipline principally developed over the past 50 years. Bibliometric methods provide quantitative analysis and identify research trends. Study aims were to characterize the growth and trends in pediatric gastroenterology clinical and translational research using citation analysis. Using citations analysis software, a search strategy specific for pediatric gastroenterology was implemented for the years 1970 to 2017. The 50 most-cited research articles per decade were identified. These 250 articles were coded for topic and study attribute. Analysis included authors, affiliations, journals, countries, and funding sources. Overall average annual growth rate for pediatric gastroenterology publications was significantly higher than that for general pediatrics (51.7% vs 6.2%; P < 0.05). Among the top 250 cited articles, the distribution of study focus was epidemiology (43%), pathophysiology (18%), treatment (16%), diagnosis (8%), prevention (8%), and comorbidities of gastrointestinal diseases (7%).There were 38 different topics represented and there was a notable shift in topic focus over time. Cholestasis, biliary atresia, and total parenteral nutrition were common topics from 1970 to 1989 and obesity, nonalcoholic fatty liver disease, and eosinophilic esophagitis were common topics after 1990. Notably, 2.3% of the authors accounted for 30% of the top 250 articles. Pediatric gastroenterology research has undergone rapid growth yielding advancements in the management of gastrointestinal conditions in children. The emergence of new diseases in need of better diagnostics and therapeutics led to a temporal shift in research focus. Further advancements will require multidisciplinary collaborations and continued funding for pediatric gastroenterology research.

Genomic Inference of Recombination-Mediated Evolution in Xanthomonas euvesicatoria and X. perforans.

Recombination is a major driver of evolution in bacterial populations, because it can spread and combine independently evolved beneficial mutations. Recombinant lineages of bacterial pathogens of plants are typically associated with the colonization of novel hosts and the emergence of new diseases. Here we show that recombination between evolutionarily and phenotypically distinct plant-pathogenic lineages generated recombinant lineages with unique combinations of pathogenicity and virulence factors. Xanthomonas euvesicatoria and Xanthomonas perforans are two closely related lineages causing bacterial spot disease on tomato and pepper worldwide. We sequenced the genomes of atypical strains collected from tomato in Nigeria and observed recombination in the type III secretion system and effector genes, which showed alleles from both X. euvesicatoria and X. perforans Wider horizontal gene transfer was indicated by the fact that the lipopolysaccharide cluster of one strain was most similar to that of a distantly related Xanthomonas pathogen of barley. This strain and others have experienced extensive genomewide homologous recombination, and both species exhibited dynamic open pangenomes. Variation in effector gene repertoires within and between species must be taken into consideration when one is breeding tomatoes for disease resistance. Resistance breeding strategies that target specific effectors must consider possibly dramatic variation in bacterial spot populations across global production regions, as illustrated by the recombinant strains observed here.IMPORTANCE The pathogens that cause bacterial spot of tomato and pepper are extensively studied models of plant-microbe interactions and cause problematic disease worldwide. Atypical bacterial spot strains collected from tomato in Nigeria, and other strains from Italy, India, and Florida, showed evidence of genomewide recombination that generated genetically distinct pathogenic lineages. The strains from Nigeria and Italy were found to have a mix of type III secretion system genes from X. perforans and X. euvesicatoria, as well as effectors from Xanthomonas gardneri These genes and effectors are important in the establishment of disease, and effectors are common targets of resistance breeding. Our findings point to global diversity in the genomes of bacterial spot pathogens, which is likely to affect the host-pathogen interaction and influence management decisions.

Gene Flow between Divergent Cereal- and Grass-Specific Lineages of the Rice Blast Fungus Magnaporthe oryzae.

ABSTRACTDelineating species and epidemic lineages in fungal plant pathogens is critical to our understanding of disease emergence and the structure of fungal biodiversity and also informs international regulatory decisions. Pyricularia oryzae (syn. Magnaporthe oryzae) is a multihost pathogen that infects multiple grasses and cereals, is responsible for the most damaging rice disease (rice blast), and is of growing concern due to the recent introduction of wheat blast to Bangladesh from South America. However, the genetic structure and evolutionary history of M. oryzae, including the possible existence of cryptic phylogenetic species, remain poorly defined. Here, we use whole-genome sequence information for 76 M. oryzae isolates sampled from 12 grass and cereal genera to infer the population structure of M. oryzae and to reassess the species status of wheat-infecting populations of the fungus. Species recognition based on genealogical concordance, using published data or extracting previously used loci from genome assemblies, failed to confirm a prior assignment of wheat blast isolates to a new species (Pyricularia graminis-tritici). Inference of population subdivisions revealed multiple divergent lineages within M. oryzae, each preferentially associated with one host genus, suggesting incipient speciation following host shift or host range expansion. Analyses of gene flow, taking into account the possibility of incomplete lineage sorting, revealed that genetic exchanges have contributed to the makeup of multiple lineages within M. oryzae. These findings provide greater understanding of the ecoevolutionary factors that underlie the diversification of M. oryzae and highlight the practicality of genomic data for epidemiological surveillance in this important multihost pathogen.